update test to constant poprtion

nf-core · Dec 3, 2024 · 7c942d8 · 7c942d8
1 parent e63d5a9
commit 7c942d8
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Showing 2 changed files with 415 additions and 76 deletions.
diff --git a/subworkflows/local/qc_workflow/test/main.nf.test b/subworkflows/local/qc_workflow/test/main.nf.test
@@ -83,51 +83,47 @@ nextflow_workflow {
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
                     ])
 
-                // ch_bam_sorted_indexed
-                input[1] = Channel.of(
-                    [
-                        [id: "chr22_bam"],
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
-                    ])
-
                 // ch_chrgtf
-                input[2] = Channel.of(
+                input[1] = Channel.of(
                     [
                         [ id: "chr22_gtf" ],
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true)
                     ])
 
                 // ch_refflat
-                input[3] = UCSC_GTFTOGENEPRED.out.refflat
+                input[2] = UCSC_GTFTOGENEPRED.out.refflat
 
                 // ch_fasta
-                input[4] = Channel.of(
+                input[3] = Channel.of(
                     [
                         [ id: "test_ref" ],
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExist: true)
                     ] )
 
                 // ch_fai
-                input[5] = Channel.of(
+                input[4] = Channel.of(
                     [
                         [ id: "test_ref" ],
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExist: true)
                     ] )
 
                 // ch rRNA interval list
-                input[6] = GATK4_BEDTOINTERVALLIST.out.interval_list
+                input[5] = GATK4_BEDTOINTERVALLIST.out.interval_list
                 """
             }
         }
 
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file( workflow.out.versions[0] ),
+                    file( workflow.out.rnaseq_metrics[0][1] ).readLines()[4..-1],
+                    file( workflow.out.duplicate_metrics[0][1] ).readLines()[4..-1],
+                    file( workflow.out.insertsize_metrics[0][1] ).readLines()[4..-1],
+                ).match() }
             )
         }
-
     }
 
 }